SMTL ID : 7xk7.1

Cryo-EM structure of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, with korormicin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.1: 18 residues within 4Å: Chain B: I.169, R.209, F.213, W.226, T.236, A.237, L.238, S.239, S.271, E.274, G.334, G.335, P.379, E.380, G.381, M.382, M.383, L.384 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274 Hydrogen bonds: B:A.237, B:L.238, B:S.271, B:E.274, B:G.335, B:E.380, B:E.380, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 pi-Cation interactions: B:R.209 FMN.8: 17 residues within 4Å: Chain B: F.213, F.214, P.217, S.221, G.222, D.223, A.377 Chain C: W.146, T.173, L.176, G.177, K.207, G.223, A.224, T.225, L.226, T.227 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:T.173, C:T.173, C:G.177, C:G.223, C:T.225, C:L.226, C:T.227, C:T.227, B:G.222, B:D.223 Salt bridges: C:K.207 Hydrophobic interactions: B:F.213, B:F.214, B:P.217

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 20 residues within 4Å: Chain B: I.56, V.60, G.158, V.161, T.162, L.165, K.191, T.197, G.198, N.200, N.203, P.204, A.205, I.292, F.342, M.343, T.345, D.346, P.347, V.348 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60, B:I.292, B:P.347 Hydrogen bonds: B:G.158, B:T.162, B:G.196, B:G.198, B:N.200, B:N.203, B:A.205, B:D.346

1 x IQT: Korormicin(Non-covalent)

IQT.3: 17 residues within 4Å: Chain A: W.337 Chain B: W.23, L.33, K.54, M.57, I.58, F.137, I.138, G.141, F.142, V.145, L.146, M.149, N.156, E.157, F.159, F.160 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.23, B:L.33, B:M.57, B:I.58, B:F.137, B:F.142, B:F.142, B:V.145, B:L.146, B:E.157, B:F.160, B:F.160, A:W.337 Hydrogen bonds: B:E.157, B:G.158, B:F.159, B:F.160 Water bridges: B:K.54 Salt bridges: B:K.54

3 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.4: 11 residues within 4Å: Chain B: W.260, F.264, L.278, M.281, A.285, W.295, I.298, G.299, M.302, H.328, L.331 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.264, B:L.278, B:W.295, B:I.298, B:L.331 Salt bridges: B:H.328 PEE.6: 6 residues within 4Å: Chain B: W.100, L.123, L.130, P.131, Y.133, A.134 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.123, B:L.130, B:L.130, B:P.131, B:Y.133, B:Y.133 PEE.10: 4 residues within 4Å: Chain C: A.28, A.29 Chain D: F.58 Chain F: M.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:F.58, F:M.1

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.5: 6 residues within 4Å: Chain B: I.306, N.313, N.324, P.326, W.327, H.328 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.306, B:I.306, B:W.327, B:W.327 Hydrogen bonds: B:N.313, B:N.324 LMT.7: 6 residues within 4Å: Chain B: W.177, L.181 Chain D: L.155, W.174, Q.176, N.178 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.155, B:W.177, B:L.181 Hydrogen bonds: D:Q.176

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 3 residues within 4Å: Chain C: Q.93, A.119, H.141 No protein-ligand interaction detected (PLIP)

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.11: 9 residues within 4Å: Chain D: G.27, C.29, N.111, C.112 Chain E: G.24, M.25, C.26, N.119, C.120 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, Metal complexes: E:C.26, E:C.120, D:C.29, D:C.112 FES.12: 9 residues within 4Å: Chain F: A.69, G.72, G.74, S.75, C.76, G.77, C.79, L.109, C.111 0 PLIP interactions:

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.13: 21 residues within 4Å: Chain F: Y.167, R.210, A.211, Y.212, S.213, N.227, V.228, R.229, T.232, P.233, P.234, V.240, P.241, P.242, G.243, Q.244, M.245, S.246, A.283, F.406, G.407 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:Y.167 Hydrogen bonds: F:A.211, F:A.211, F:S.213, F:N.227, F:R.229, F:Q.244, F:M.245, F:S.246, F:F.406 Salt bridges: F:R.210, F:R.210 pi-Stacking: F:Y.212, F:F.406, F:F.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishikawa, J.I. et al., Cryo-EM structures of Na + -pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae. Nat Commun (2022)

Release Date

2022-07-20

Peptides

Na(+)-translocating NADH-quinone reductase subunit A: A
Na(+)-translocating NADH-quinone reductase subunit B: B
Na(+)-translocating NADH-quinone reductase subunit C: C
Na(+)-translocating NADH-quinone reductase subunit D: D
Na(+)-translocating NADH-quinone reductase subunit E: E
Na(+)-translocating NADH-quinone reductase subunit F: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Na(+)-translocating NADH-quinone reductase subunit A

Na(+)-translocating NADH-quinone reductase subunit B

Na(+)-translocating NADH-quinone reductase subunit C

Na(+)-translocating NADH-quinone reductase subunit D

Na(+)-translocating NADH-quinone reductase subunit E

Na(+)-translocating NADH-quinone reductase subunit F

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